Closed KatyBrown closed 3 weeks ago
Additionally, the link to tutorial.ipynb
in the paper is broken (points to root of repo, not to the demo dir).
Hi @KatyBrown and @kdm9!
I have updated the version of fraggler on pypi. The tutorial works for me when I pip install the latest version of fraggler. Try it out and let me know if it still does not work.
William
Thank you, the tutorial works nicely now.
Issue raised as part of the JOSS review process to address the "Functionality" check https://github.com/openjournals/joss-reviews/issues/6869
In the demo Jupyter notebook, some of the commands do not work with the version of the code currently on pip - I think the final three functions in
fraggler.py
-fit_ladder
,find_peaks
andfit_area
must be elsewhere in that version as there are ImportErrors for these functions.I therefore cloned the git repo directly and imported fraggler.fraggler from the cloned folder but this led to different errors - I would guess that the
fraggler.FsaFile
function has some different parameters in the current version of the code on GitHub than in the tutorial, as it expectedsample_channel
,min_distance_between_peaks
andmin_size_standard_height
to be specified but they are not in the notebook, and it didn't recognisetrace_channel
.I didn't progress past that point but it seems like the tutorial for the Python version of the code needs updating to be usable.